Contacts of the strand formed by residues 130 - 139 (chain A) in PDB entry 4QAE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.4 24.7 - - + -
40A GLU* 2.6 42.4 + - - -
125A VAL 3.6 0.2 - - - +
126A VAL* 3.4 5.2 - - - +
127A TRP* 2.9 64.5 + - - +
128A GLN* 4.4 11.3 + - - +
129A ASN* 1.3 79.4 - - - +
131A GLU* 1.3 66.6 + - - +
132A VAL* 3.9 6.1 + - + +
13P CYS* 3.1 20.2 + - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 6.1 1.0 - - - +
8A ILE 4.7 0.7 - - - +
9A PRO* 5.7 0.2 - - - +
10A ALA* 3.7 34.2 + - + +
39A ASN* 3.1 18.7 + - - -
40A GLU* 5.0 1.0 - - - +
124A LYS* 2.9 33.2 + - + -
125A VAL 3.3 7.0 - - - +
126A VAL* 4.5 14.8 - - + +
130A ARG* 1.3 81.7 - - - +
132A VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN* 3.5 11.2 - - - +
40A GLU* 3.6 36.1 - - + +
124A LYS* 3.2 2.9 - - - +
125A VAL* 2.7 40.2 + - + +
127A TRP* 4.2 10.3 - - + -
130A ARG* 4.0 10.5 - - + +
131A GLU* 1.3 76.5 - - - +
133A PHE* 1.3 63.3 + - - +
134A TRP* 4.1 3.1 - - + -
10P CYS* 3.6 13.0 - - - -
11P CYS 3.6 23.8 - - - +
13P CYS* 3.7 21.3 - - - +
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Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 4.4 1.6 - - + -
9A PRO 3.5 20.2 - - - -
10A ALA* 3.7 16.2 - - + -
11A PRO* 3.9 9.0 - - + -
38A GLY* 3.2 2.4 - - - -
39A ASN* 2.9 60.5 + - + +
40A GLU 4.6 0.7 + - - -
122A PHE* 3.6 28.5 - + + -
123A PHE 3.1 14.6 - - - +
124A LYS* 4.2 5.6 - - + -
132A VAL* 1.3 76.5 - - - +
134A TRP* 1.3 72.4 + - - +
135A VAL* 5.0 0.2 - - + -
159A LEU* 3.8 29.8 - - + -
161A LEU* 3.6 39.3 - - + -
11P CYS 5.0 0.7 - - - +
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Residues in contact with TRP 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.5 27.6 - - + -
37A ALA 2.9 16.8 - - - +
38A GLY* 3.9 4.7 - - - -
41A VAL* 5.0 0.7 - - + -
52A TRP* 4.9 1.8 - - - -
81A GLN* 6.2 0.2 - - - -
122A PHE* 3.6 2.1 - - - -
123A PHE* 2.8 76.9 + + + +
125A VAL* 3.9 15.7 - - + -
132A VAL 4.1 12.3 - - - -
133A PHE* 1.3 87.4 - - - +
135A VAL* 1.3 61.6 + - - +
136A THR* 4.2 6.7 - - + +
9P PHE* 3.6 26.6 - + - -
10P CYS* 3.5 30.1 - - - -
11P CYS* 3.7 44.4 - - + +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.4 5.9 - - - +
37A ALA 2.7 35.9 + - - +
120A MET* 4.6 2.5 - - + -
121A VAL 3.2 15.9 - - - +
122A PHE* 4.2 8.5 - - + -
133A PHE* 5.0 2.9 - - + -
134A TRP* 1.3 78.3 - - - +
136A THR* 1.3 69.0 + - - +
152A PHE* 3.6 23.6 - - + -
155A PHE* 3.9 26.5 - - + -
156A SER* 4.5 6.7 - - - +
159A LEU* 3.7 29.4 - - + -
161A LEU* 5.1 4.3 - - + -
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.1 14.1 - - + -
35A GLY 3.4 4.9 - - - -
36A LEU* 4.0 17.7 - - + -
52A TRP* 4.4 7.6 - - + -
119A ALA 3.7 0.3 - - - +
120A MET* 3.2 7.1 - - - +
121A VAL* 2.8 33.9 + - - +
123A PHE* 3.4 25.2 - - + -
134A TRP* 4.2 5.1 - - + -
135A VAL* 1.3 77.4 - - - +
137A LEU* 1.3 58.8 + - - +
138A TYR* 3.1 37.0 + - + +
152A PHE* 4.2 2.5 - - - -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR 3.7 0.2 - - - +
33A VAL* 3.7 1.4 - - - -
34A VAL* 2.8 39.5 + - + -
35A GLY* 2.8 18.5 + - - +
118A HIS* 4.9 7.0 - - + +
119A ALA 3.4 14.6 - - - +
120A MET* 3.9 15.0 - - + -
136A THR* 1.3 70.1 - - - +
138A TYR* 1.3 56.3 + - - +
144A LEU* 3.7 27.4 - - + -
148A LEU* 4.0 10.3 - - + +
149A LYS* 4.0 28.3 - - + +
152A PHE* 3.7 38.4 - - + -
168A PHE* 4.6 2.7 - - + -
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Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 4.0 7.0 - + - -
31A TRP* 3.5 35.9 - + + -
32A TYR 3.2 11.0 - - - -
33A VAL* 4.0 15.5 - - + -
54A THR* 3.8 17.8 + - - +
56A TYR* 2.7 45.5 + + - -
118A HIS* 3.2 9.0 - - - +
119A ALA* 2.8 37.5 + - + +
121A VAL* 3.5 24.2 - - + -
123A PHE* 3.5 13.0 - - - -
136A THR* 3.1 33.3 - - + +
137A LEU* 1.3 73.8 - - - +
139A GLY* 1.3 58.9 + - - +
144A LEU* 3.6 6.6 - - - +
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Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TRP* 3.6 6.9 - - - -
32A TYR 2.8 36.6 + - - -
34A VAL* 4.0 3.4 - - - +
117A GLN 3.3 8.3 - - - -
138A TYR* 1.3 74.1 - - - +
140A ARG* 1.3 64.7 + - - -
141A THR 3.1 16.6 - - - +
144A LEU* 4.1 12.6 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il